Fix/feature

[teslajoy]

Specimen Enhancements:

• Added a parent reference to the Specimen resource.
• Implemented a function to create an Organization for the Specimen collector reference, capturing a hierarchy of Lab (“sub_organization”)-> Lab (“sub_organization”)-> Organization.

Observation Enhancements:

• Introduced a general Observation code for Specimens, used when no code exists or is not captured through Jinja templates.
• Enhanced Observation.component handling to support a list of CodeableReferences instead of creating one Observation per a general context.
• Fixed the Observation.focus reference to correctly point to the entity that the Observation components focus is on.

Specimen Identifiers:

• Added support for multiple identifiers for Specimen resources. Needs to be generalized to all FHIR entities in the next PRs.

MedicationAdministration to SubstanceDefinition:

• Added support for Substance and SubstanceDefinition resources, based on drug names found in the ChEMBL database (version 34, located at ./resources/chembl/chemble_34.db).
• Created a workflow linking MedicationAdministration -> Medication -> Substance -> SubstanceDefinition entities in FHIR.
  Note: The current workflow involves SQL-based searches in ChEMBL per row and includes regimen and index start date days identifiers that are use-case specific. It’s the functional workflow etl, it is not ideal and could be optimized in future PRs.

[teslajoy]

this goes hand in hand with fhir_labkey